The 19-year-old defender has been added to the squad for Tuesday night's clash with Leyton Orient.
Flanagan joined Kettering at the turn of the year and was due to stay with the Blue Square Premier side until March 3.
However, Dons boss Karl Robinson has opted to bring a premature end to his spell at Rockingham Road to give his thin squad a boost.
Sean O'Hanlon played against Brentford on Saturday despite not being fully fit, while Gary MacKenzie is still suspended and Dan Woodards missed out with an injury.
Flanagan made eight appearances for the Poppies and scored one goal.